Term
| types of GENETIC MATERIAL TRANSFER |
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Definition
-vertical transmission
-horizontal transmission |
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Term
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Definition
| genetic material transfer from parent to offspring |
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Term
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Definition
| Transfer of small pieces of DNA from one cell to another |
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Term
| Bacterial Chromosomes Are Compacted into a... |
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Definition
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Term
| the normal pH of the E. coli cell |
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Definition
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Term
| DNA is the second-largest molecule in the bacterial cell (only ______ is larger) |
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Definition
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Term
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Definition
| series of protein-bound domains that bacteria pack their DNA into |
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Term
| Studied Streptococcus pneumoniae in mice |
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Definition
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Term
| Hypothesized that the bacteria Streptococcus pneumoniae could “transfer information” to each other. |
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Definition
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Term
| What does the "Smooth (S)" strain of Streptococcus pneumoniae do to the host? |
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Definition
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Term
| What does the "Rough (R)" strain of Streptococcus pneumoniae do to the host? |
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Definition
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Term
| What do Pre-killing "S" strains of Streptococcus pneumoniae do to the host? |
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Definition
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Term
| What does the combination of killed "(S)" and live (R) strains of Streptococcus pneumoniae do to the host? |
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Definition
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Term
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Definition
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Term
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Definition
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Term
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Definition
| mouse contracts pneumonia |
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Term
|
Definition
| S colonies isolated from tissue of dead mouse |
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Term
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Definition
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Term
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Definition
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Term
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Definition
| R colonies isolated from tissue |
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Term
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Definition
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Term
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Definition
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Term
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Definition
| no colonies isolated from tissue |
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Term
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Definition
| living R cells plus heat-killed S cells |
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Term
|
Definition
| mouse contracts pneumonia |
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Term
|
Definition
| R and S colonies isolated from tissue of dead mouse |
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Term
| shape of most bacterial genomes |
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Definition
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Term
|
Definition
| Horizontal gene transfer requiring cell contact. Genes transferred sequentially. |
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Term
|
Definition
| movement of “free DNA” into a live cell |
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Term
| difference between conjugation and transformation |
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Definition
| Transformation is movement of “free DNA” into a live cell. Conjugation requires two live cells physically contacting each other. |
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Term
| how bacteria come together to begin conjugation |
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Definition
-The two cells are brought together by the pilus on the donor.
-The two cells then come closer together by the pilus on the donor. |
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Term
|
Definition
| an enzyme that nicks DNA to relax it to allow for its movement from one bacterium to another in the conjugation process. One DNA strand is transferred. The donor also keeps a strand for itself so it doesn’t lose the genetic information. |
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Term
| what happens at the completion of conjugation? |
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Definition
| the recipient bacteria now becomes a donor |
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Term
| size of PROKARYOTIC GENOMES |
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Definition
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Term
|
Definition
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Term
| amount of non-coding DNA in prokaryotic genomes |
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Definition
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Term
| amount of non-coding DNA in human genome |
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Definition
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Term
|
Definition
1: The two cells are brought together by the pilus on the donor.
2: The two cells are brought closer together by the pilus on the donor.
3: Relaxase assists in the DNA transfer by nicking one DNA strand to relax it to allow for its movement from one bacterium to another.
4: the recipient bacteria now becomes a donor.
[image] |
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Definition
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Definition
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Definition
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Definition
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Definition
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Definition
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Definition
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Term
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Definition
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Term
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Definition
| units of information composed of a sequence of DNA nucleotides |
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Term
|
Definition
| a group of genes that exist in tandem with each other, situated from head to tail. The entire operon is controlled by a single regulatory sequence located in front of the first gene. |
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Term
| The entire operon is controlled by... |
|
Definition
| a single regulatory sequence located in front of the first gene. |
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Term
|
Definition
[image]
the yellow is a single gene, but the green is an operon |
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Term
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Definition
| RNA that codes for one protein |
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Term
|
Definition
| RNA that codes for more than one protein |
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Term
| single gene produces monocistronic or polycistronic RNA? |
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Definition
|
|
Term
| operon produces monocistronic or polycistronic RNA? |
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Definition
|
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Term
|
Definition
a collection of genes or operons with a unified biochemical purpose. They can occur on different parts of the chromosome, but they're regulated by the same regulatory protein.
[image] |
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Term
| A supercoil can be introduced into a double-stranded, circular DNA molecule by... |
|
Definition
(1) cleaving both strands at one site in the molecule
(2) passing an intact part of the molecule between ends of the cut site
(3) reconnecting the free ends.
[image] |
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Term
| the 2 types of supercoils |
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Definition
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Term
|
Definition
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Term
|
Definition
|
|
Term
| organisms that positively supercoil their DNA |
|
Definition
| archaeans living in acid at high temperature |
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Term
| why archaeans living in acid at high temperature have positively supercoiled DNA |
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Definition
| to make it harder to denature, because it takes excess energy to separate overwound DNA |
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Term
| organisms that negatively supercoil their DNA |
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Definition
-bacteria
-archaea
-eukaryotes |
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Term
|
Definition
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Term
| the 2 types of topoisomerases |
|
Definition
|
|
Term
|
Definition
-Usually single proteins
-Cleave one strand of DNA |
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Term
|
Definition
-Have multiple subunits
-Cleave both strands of DNA (“ds break”) |
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|
Term
| example of type II topoisomerase |
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Definition
|
|
Term
| ______ is targeted by quinolone antibiotics |
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Definition
|
|
Term
| DNA gyrase is targeted by ______ antibiotics |
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Definition
|
|
Term
| how type I topoisomerase supercoils DNA |
|
Definition
1: Topoisomerase I cleaves one strand of a double helix, holds on to both ends, and . . .
2: . . . passes the other, intact strand through the break and re-ligates the strand.
3: The helix winds in this region, resulting in one less negative supercoil.
[image] |
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|
Term
| Topoisomerase I relaxes a negatively supercoiled DNA molecule by... |
|
Definition
| introducing a single-strand nick. |
|
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Term
|
Definition
| how spatial features of an object are connected to each other |
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|
Term
| where topoisomerases get their name |
|
Definition
| they change the topology of DNA |
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|
Term
| how type II topoisomerase supercoils DNA |
|
Definition
1: GyrB grabs one section of double-stranded DNA (represented by cylinder).
2: GyrA introduces double-strand break in this section (cylinder) and holds the two ends apart while remaining covalently attached to the DNA.
3: GyrA ATPase passes the intact double-stranded section through the double-strand break.
4: GyrA re-joins the cleaved DNA and opens at the other end to allow the strand that has passed through to exit.
[image] |
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Term
| how gyrase supercoils DNA |
|
Definition
1: Gyrase grabs one section and introduces a ds break.
2: It then passes the intact strand through the ds break. |
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Term
|
Definition
| where DNA replication begins |
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|
Term
| how bacterial DNA replicates |
|
Definition
1. Replication begins at origin.
2. Replication bubble forms. Replication forks progress in opposite directions.
3. One strand at each fork is synthesized continuously 5′ to 3′.
4. Second strand at each fork is synthesized discontinuously in Okazaki fragments 5′ to 3′.
5. Replication ends at terminus.
[image] |
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Term
| 2 molecules that regulate DNA replication in E. coli |
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Definition
|
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Term
|
Definition
| initiates replication in E. coli |
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Term
|
Definition
| inhibits replication in E. coli |
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|
Term
| SeqA has an affinity for... |
|
Definition
|
|
Term
| does E. coli methylate its own DNA? |
|
Definition
|
|
Term
| does freshly made E. coli DNA have methyl groups? |
|
Definition
| just after replication, there is a short period before methyl groups can be added to new strand. |
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|
Term
| As the cell grows, DnaA levels ______. |
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Definition
|
|
Term
| ______ bind to 9-bp repeats upstream of the origin (oriC). |
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Definition
|
|
Term
| DnaA-ATP complexes bind to ______ upstream of the origin (oriC). |
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Definition
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|
Term
| DnaA-ATP complexes bind to 9-bp repeats upstream of the ______. |
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Definition
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|
Term
| Binding of DnaA-ATP complexes causes DNA to... |
|
Definition
| prepare for being melted open by the helicase (DnaB). |
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Term
|
Definition
| the helicase that melts open DNA in E. coli |
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|
Term
| E. coli has how many DNA polymerases? |
|
Definition
|
|
Term
| all the DNA polymerases in E. coli catalyze DNA synthesis in what direction? |
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Definition
|
|
Term
| The main replication polymerase in E. coli |
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Definition
|
|
Term
|
Definition
| The main replication polymerase in E. coli |
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Term
| DNA Pol III can also scan for... |
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Definition
|
|
Term
| this DNA polymerase can scan for mismatched bases in E. coli |
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Definition
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|
Term
| Mismatching of bases causes... |
|
Definition
| cleavage of the phosphodiester bond on the mismatched base (exonuclease activity). |
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Term
|
Definition
cleavage of the phosphodiester bond on the mismatched base
Once removed, elongation resumes. |
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Term
|
Definition
| cells use this to remove RNA primers |
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Term
|
Definition
| After the removal of RNA primers, this repairs the phosphodiester nick using energy from NAD (in bacteria) or ATP (in eukaryotes). |
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|
Term
| WHAT HAPPENS TO THE RNA PRIMERS in bacteria? |
|
Definition
1: To remove RNA primers, cells use RNase H.
2: A DNA Pol I enzyme then synthesizes a DNA patch using the 3′ OH end of the preexisting DNA fragment as a priming site.
3: Finally, DNA ligase repairs the phosphodiester nick using energy from NAD (in bacteria) or ATP (in eukaryotes). |
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|
Term
| DNA ligase repairs the phosphodiester nick using energy from ______ (in bacteria) or ______ (in eukaryotes). |
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Definition
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|
Term
| DNA ligase repairs the phosphodiester nick using energy from NAD (in ______) or ATP (in ______). |
|
Definition
|
|
Term
|
Definition
| In terminating DNA replication, this catalyzes a breaking and re-joining event that resolves the link. |
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|
Term
| how DNA replication in bacteria is terminated |
|
Definition
1: Replication forms a linked catenane of sister chromosomes.
2: XerCD passes linked chromosomes through each other, forming a catenane.
3: Topoisomerase IV catalyzes a breaking and re-joining event that resolves the link.
[image] |
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Term
|
Definition
| An extrachromosomal genetic element that may be present in some cells. |
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Term
| some characteristics of plasmids |
|
Definition
-smaller than chromosomes
-Found in bacteria, archaea, and eukaryotic microbes
-Circular
-Separate Ori
-Primarily encode genes for survival |
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Term
|
Definition
-bacteria
-archaea
-eukaryotic microbes |
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|
Term
| plasmids primarily encode... |
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Definition
|
|
Term
| What are some examples of genes that plasmids might carry? |
|
Definition
-antibiotic resistance
-pathogenesis
-environmental survival |
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|
Term
| advantage of plasmid conferring antibiotic resistance |
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Definition
| with this being on a plasmid, bacteria can quickly replicate and produce this as needed |
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Term
|
Definition
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|
Term
| why bacteria can cause sickness |
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Definition
| because some genes they use just happen to make the host sick |
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Term
| advantage of plasmid conferring environmental survival |
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Definition
| this helps it survive in environments it’s usually not in |
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Term
| tricks plasmids have to ensure their inheritance |
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Definition
-Low-copy-number plasmids segregate equally to daughter cells.
-High-copy-number plasmids segregate randomly to daughter cells. |
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Term
|
Definition
| segregate equally to daughter cells |
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|
Term
| High-copy-number plasmids |
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Definition
| segregate randomly to daughter cells |
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Term
| some conditions plasmids are advantageous under |
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Definition
-Resistance to antibiotics and toxic metals
-Pathogenesis
-Symbiosis |
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Term
| Plasmids are useful for... |
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Definition
| genetic engineering applications. |
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Term
| one way bacteria rid themselves of foreign DNA |
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Definition
| restriction endonucleases |
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Term
| restriction endonucleases |
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Definition
| “Molecular scissors” that cleave unfamiliar DNA molecules at specific palindromic sequences called restriction sites |
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|
Term
| restriction endonucleases aka... |
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Definition
|
|
Term
|
Definition
| specific palindromic sites where restriction endonucleases cleave unfamiliar DNA molecules |
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Term
| what humens use restriction endonucleases for |
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Definition
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Term
| scenario in which a bacteria would want to use restriction enzymes to cut foreign DNA |
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Definition
| protection, often against viral DNA (bacteriophages) |
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Term
| how bacteria avoid cutting their own DNA |
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Definition
| they methylate their DNA at specific sequences where they would otherwise be cut |
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Term
|
Definition
| sequence where both strands read the same in the 5’-3’ direction |
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Term
| how restriction enzymes are named |
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Definition
| their names reflect the genus and species of the source organism |
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Term
| 2 types of ends that can be caused by restriction endonucleases |
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Definition
-blunt (no overhang)
-sticky (has overhang) |
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Term
| how recombinant DNA molecules are formed |
|
Definition
1. Plasmid and foreign DNA are cut with a restriction endonuclease (EcoRI) to produce identical cohesive ends.
2. Cut vector and foreign DNA fragments are mixed. Cohesive ends anneal.
3. DNA ligase seals the nicks.
[image] |
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Term
| ______ can be used to analyze fragments of DNA cut after cleavage with restriction endonucleases. |
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Definition
|
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Term
|
Definition
| the process of importing free DNA into bacterial cells |
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Term
|
Definition
| Able to take up DNA from the environment (capable of natural transformation) |
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Term
| how bacteria are artificially manipulated to undergo transformation |
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Definition
| by perturbing the membrane by chemical (CaCl2) or electrical (electroporation) methods |
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Term
|
Definition
| subject (a system, moving object, or process) to an influence tending to alter its normal or regular state or path |
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Term
| how CaCl2 enables a bacterium to undergo transformation |
|
Definition
| it alters the membrane, making these cells chemically competent so that DNA can pass |
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Term
| In a natural environment, what would be the advantage of a bacteria being competent? |
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Definition
| enhances survival by being able to acquire the necessary genes |
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Term
|
Definition
| A bacterial cell membrane protein complex that imports external DNA during transformation in Gram positive bacteria. It facilitates uptake of DNA. |
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Term
| the DNA taken in by the transformasome complex |
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Definition
| ssDNA; it takes in one strand while degrading the other |
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|
Term
| The process of transformation in competent bacteria begins with... |
|
Definition
| the synthesis of a signaling molecule (competence factor, CF) |
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|
Term
| The process of transformation in competent bacteria concludes with... |
|
Definition
| the import of a single-stranded DNA strand through a transformasome complex |
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|
Term
| how Gram positive bacteria undergo transformation |
|
Definition
1. Precursor to competence factor (CF) is made and cleaved, and active CF is secreted.
2. As cell numbers rise, external CF level increases and activates ComD sensor kinase.
3. Phosphate from ComD is transferred to ComE. ComE-P stimulates sigma factor H (SigH) transcription.
4. SigH directs transcription of transformasome components.
5. Transformasome binds extracellular DNA. One strand is transported; one strand is degraded.
[image] |
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Term
| Competence in Gram positive bacteria is generated by... |
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Definition
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|
Term
| As the Gram positive bacteria grow, the competence factor (CF)... |
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Definition
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|
Term
| In Gram positive bacteria, at specific levels, CF will induce... |
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Definition
| a genetic program that induces the transformasome |
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Term
| Gram-negative bacteria transform DNA without... |
|
Definition
| the use of competence factors (CF) |
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Term
| when Gram-negative bacteria are competent |
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Definition
| Either they are always competent or they become competent when starved. |
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Term
| Do Gram-negative bacteria use transformasomes? |
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Definition
|
|
Term
| specificity of transformation in most Gram-negative species |
|
Definition
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|
Term
| Why is gene exchange limited between genera of Gram-negative bacteria? |
|
Definition
| because transformation in most Gram-negative species is sequence specific |
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Term
| 2 ways genes can be transferred between bacteria |
|
Definition
-transformation
-conjugation |
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|
Term
| GENE TRANSFER BY CONJUGATION requires... |
|
Definition
| the presence of special transferable plasmids |
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|
Term
| transferrable plasmids that are transferred by conjugation usually contain... |
|
Definition
| all the genes needed for pilus formation and DNA export |
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|
Term
| example of a gene needed for pilus formation and DNA export |
|
Definition
| E. coli fertility factor (F) |
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|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
| Membrane proteins encoded by F+ bacteria prevent... |
|
Definition
| conjugation with other F+ |
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|
Term
| The relaxosome complex is composed of... |
|
Definition
| TraH, TraI (the helicase/ endonuclease), TraJ, and TraK |
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|
Term
| the helicase in gene transfer by conjugation |
|
Definition
|
|
Term
| the endonuclease in gene transfer by conjugation |
|
Definition
|
|
Term
| how gene transfer by conjugation occurs |
|
Definition
1. Sex pilus from the F+ plasmid donor (left) attaches to receptors on the recipient cell (right).
2. Contraction of the pilus draws the two cells together and forms a relaxosome bridge.
3. The F factor is nicked at oriT, and the 5′ end begins transfer through the bridge.
4. The strand remaining in the donor is replicated.
5. Once in the recipient, the transferred strand circularizes and replicates.
6. The recipient has been converted to a donor.
[image] |
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Term
|
Definition
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Term
|
Definition
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Term
|
Definition
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Term
|
Definition
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Term
|
Definition
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Term
|
Definition
|
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Term
|
Definition
| Relaxase nicks DNA at oriT (nic site) |
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Term
|
Definition
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|
Term
|
Definition
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Term
|
Definition
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Term
|
Definition
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Term
|
Definition
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Term
|
Definition
|
|
Term
| how the ssDNA moves through the pore into the recipient |
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Definition
| The 5′ end of the nick will move through the pore and remain attached to the membrane while the rest of the single-stranded DNA passes into the recipient. |
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Term
| example of DNA transfer From Human to Bacteria |
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Definition
| Neisseria gonorrhoeae contain human-derived sequences. |
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|
Term
| example of DNA transfer From Bacteria to Plants |
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Definition
| Agrobacterium tumefaciens transfers DNA to plants. |
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Term
| Does Agrobacterium tumefaciens stimulate nodule formation or fix nitrogen? |
|
Definition
|
|
Term
| what Agrobacterium tumefaciens does to host plants |
|
Definition
-Invades crown, stems, sometimes roots of many plants.
-Transform infected plant cells into tumors. |
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Term
| why Agrobacterium tumefaciens causes tumors |
|
Definition
| because it contains a tumor-inducing plasmid (Ti) that can be transferred via conjugation to plants |
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Term
|
Definition
| tumor-inducing plasmid that Agrobacterium tumefaciens can transfer to plants via conjugation |
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Term
| Agrobacterium tumefaciens causes... |
|
Definition
Crown gall disease tumor
[image] |
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Term
| characteristics of CROWN GALL DISEASE |
|
Definition
-Round tumor growths on stems or roots.
-Interferes with plants ability to move nutrients and water.
-Plant severely growth impaired. |
|
|
Term
| how Agrobacterium tumefaciens causes crown gall disease in plants |
|
Definition
-Bacteria enter plants through wound/injured plant cells. They detect signals from “wound compounds”
-Transfers Ti plasmid to plant.
-Gene stimulates plant hormone production and cell division |
|
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Term
| how Agrobacterium tumefaciens knows plant is wounded |
|
Definition
| it detects “wound compounds” |
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|
Term
| Agrobacterium tumefaciens metabolizes... |
|
Definition
|
|
Term
|
Definition
| CROWN GALL DISEASE caused by Agrobacterium tumefaciens |
|
|
Term
| treatments for CROWN GALL DISEASE |
|
Definition
-Destroy infected plant
-Prune infected stem(s)
-Treat roots with control bacteria |
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|
Term
| the control bacteria used to treat roots with crown gall disease |
|
Definition
| Agrobacterium radiobacter |
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|
Term
| Agrobacterium radiobacter |
|
Definition
a non-pathogenic competitor of Agrobacterium tumefaciens
-it is the control bacteria used to treat roots with crown gall disease |
|
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Term
| how Agrobacterium radiobacter counteracts Agrobacterium tumefaciens |
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Definition
| Agrobacterium radiobacter outcompetes Agrobacterium tumefaciens for space and nutrients and eventually limits the growth of A. tumefaciens. |
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Term
|
Definition
| the process in which bacteriophages carry host DNA from one cell to another |
|
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Term
| 2 basic types of transduction |
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Definition
-Generalized transduction
-Specialized transduction |
|
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Term
|
Definition
| can transfer any gene from a donor to a recipient cell |
|
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Term
|
Definition
| can transfer only a few closely linked genes between cells |
|
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Term
| how generalized transduction occurs |
|
Definition
1. P22 phage DNA infects a host cell and makes subunit components for more phage.
2. DNA is packaged into capsid heads. Some capsids packages host DNA.
3. New phage assembly is completed.
4. Cell lyses; phage is released.
5. Transducing phage particle injects host DNA into new cell, where it may recombine into the chromosome.
[image] |
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Term
| The number of genes transferred in any one phage capsid is limited to... |
|
Definition
| what can fit in the phage head. |
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Term
|
Definition
| a heritable change in DNA |
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Term
|
Definition
| A substances that causes DNA mutations |
|
|
Term
| examples of mutagenic agents |
|
Definition
|
|
Term
|
Definition
| A test of the mutagenicity of a substance |
|
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Term
|
Definition
| Salmonella defective in hisG |
|
|
Term
| what does it mean when Salmonella is defective in hisG? |
|
Definition
| it means it's a mutant of wild-type Salmonella that cannot grow on media lacking histidine |
|
|
Term
| If Salmonella hisG suddenly grows on this histidine-free media, it means... |
|
Definition
| they acquired changes to their DNA such that it reverted the gene back to normal. This is called reversion. |
|
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Term
|
Definition
| A mutation that changes a previous mutation back to its original state |
|
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Term
|
Definition
| bacteria that has undergone reversion, which is the change of a previous mutation back to its original state |
|
|
Term
|
Definition
-A hisG auxotrophic mutant of Salmonella enterica will not grow on histidine-free medium.
-A disk containing a possible mutagen is placed at the center of the plate.
-Prototrophic hisG+ revertants form around the disk as the mutagen diffuses into the medium. [image] |
|
|
Term
| the purpose of the Ames test |
|
Definition
| to screen for mutagenesis |
|
|
Term
| why screening for mutagenesis is important |
|
Definition
| because mutagenesis is an uderlying factor in tumor and cancer development |
|
|
Term
| why the Ames test uses histidine-free media with Salmonella hisG (unable to produce histidine) |
|
Definition
| screens for revertants that mutate back to Salmonella WT |
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|
Term
|
Definition
| Ames test where liver enzymes are added to the media to determine whether or not they promote mutations |
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|
Term
A mutagen-containing disk is placed on an agar plate with the mutant.
Mutagen causes reversion mutations, and colonies start to appear around the disk.
Q- What does this tell you about the test mutagen? |
|
Definition
| it causes a significant amount of DNA damage |
|
|
Term
|
Definition
-Chief detoxifying organ of the human body
-Chemically modify foreign substances |
|
|
Term
| modified Ames tests for... |
|
Definition
| the mutagenic properties of chemicals processed through the liver |
|
|
Term
| how the modified Ames test is conducted |
|
Definition
1: The potential mutagen, his-mutant bacteria, and liver homogenate are combined and mixed with agar.
2: The combination is poured into a petri plate.
3: If the liver extract enzymes act on the test compound and the metabolites produced are mutagenic, then increasing numbers of His+ revertants will be observed with increasing doses of mutagen. If the compound is not mutagenic, few relevant colonies will be seen on any plate. [image] |
|
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Term
|
Definition
|
|
Term
| 2 types of Error-proof pathways |
|
Definition
-Methyl mismatch repair
-Nucleotide excision repair |
|
|
Term
|
Definition
| corrects unmethylated daughter strand based on the methylated parental strand so that the unmethylated daughter strand complements the methylated parental strand |
|
|
Term
| how methyl mismatch repair differentiates between parent and daughter strands of DNA |
|
Definition
| it uses methylation of the parental strand to discriminate from newly replicated DNA |
|
|
Term
| the premise of Methyl mismatch repair |
|
Definition
| The premise is that the parental strand will contain the proper DNA sequence. |
|
|
Term
|
Definition
| The methyl-directed mismatch repair proteins (and genes) |
|
|
Term
| A high mutation rate results in... |
|
Definition
| strains that are defective in certain Mut proteins. |
|
|
Term
| how methyl mismatch repair works |
|
Definition
1. MutS binds DNA mismatch.
2. MutS draws MutHL to the site to form MutHLS complex.
3. MutHLS complex causes looping
4. MutH cleaves the unmethylated strand
[image] |
|
|
Term
| NUCLEOTIDE EXCISION REPAIR |
|
Definition
| An endonuclease removes a patch of single-stranded DNA containing damaged bases. New, correctly base-paired DNA is synthesized by DNA polymerase I. |
|
|
Term
| does nucleotide excision repair distinguish between parental/daughter strands? |
|
Definition
|
|
Term
|
Definition
| The nucleotide excision repair proteins (and genes) |
|
|
Term
| how nucleotide excision repair works |
|
Definition
1: UvrA & B form a complex that binds to damaged DNA
2: UvrA bends the DNA.
3: UvrA gets ejected.
4: UvrB recruits UvrC
5: UvrC cleaves at sites that flank the damage
6: UvrD has helicase activity that strips away the damaged DNA
7: DNA Pol I fills the gap.
8: DNA ligase seals the new DNA to the 5′ end of the preexisting strand.
[image] |
|
|
Term
| transcription coupled repair |
|
Definition
| mechanism by which polymerases that stall during transcription can recruit Uvr proteins |
|
|
Term
| when Error-prone repair pathways operate |
|
Definition
| only when damage is so severe that the cell has no other choice but to mutate or die |
|
|
Term
| Error-prone repair pathways |
|
Definition
| Risk introducing mutations |
|
|
Term
| SOS (“SAVE OUR SHIP”) REPAIR |
|
Definition
I think this is another name for Error-prone repair pathways
-Induced by extensive DNA damage.
-Polymerase actions are “sloppy” because they lack the capacity for proofreading.
-However, they will replicate “through anything” to have a chance at survival.
-This is not a single mechanism but a collaborative effort. |
|
|
Term
| SOS (“SAVE OUR SHIP”) REPAIR is induced by... |
|
Definition
|
|
Term
| Polymerase actions in SOS (“SAVE OUR SHIP”) REPAIR are “sloppy” because... |
|
Definition
| they lack the capacity for proofreading. |
|
|
Term
|
Definition
| a protein that will regularly monitor the level of single stranded DNA. |
|
|
Term
| ______ can introduce many single stranded “gaps”. |
|
Definition
| Extensive UV light exposure |
|
|
Term
| Extensive UV light exposure can introduce many ______. |
|
Definition
|
|
Term
|
Definition
| a protein that prevents DNA repair gene transcription (repressor) |
|
|
Term
|
Definition
| A regulatory protein that can bind to a specific DNA sequence and inhibit transcription of genes |
|
|
Term
|
Definition
| During extensive DNA damage |
|
|
Term
| During extensive DNA damage,... |
|
Definition
|
|
Term
| what happens to cell division in SOS repair? |
|
Definition
|
|
Term
| some SOS proteins that are synthesized |
|
Definition
-Pol IV
-Pol V
-these are both “sloppy” polymerases |
|
|
Term
| Cell will live after SOS repair if... |
|
Definition
| it can tolerate any mutations caused by PolIV and Pol V…and any other side effects of the cellular stress (ie. phage activation) |
|
|
Term
| a side effect that may occur as a result of SOS repair |
|
Definition
|
|
Term
| why SOS repair may not always lead to survival and DNA repair |
|
Definition
because it activates multiple pathways
Some stress pathways may be activated and inadvertently harm the cell |
|
|
Term
| example of SOS repair leading to harming the cell |
|
Definition
| Some stress pathways may be activated and inadvertently harm the cell |
|
|
Term
| example of a stress pathway triggering SOS repair and resulting in something bad |
|
Definition
-Many humans carry Staphylococcus aureus in their nasopharynx.
-Competing bacteria (Streptococcus pneumoniae) can destroy Staph. aureus DNA, evidently by way of toxic compounds.
-SOS response is triggered.
-The SOS response activates resident phages (viruses) of Staph. aureus! Staph. aureus is killed…but Strep. pneumoniae survive… |
|
|
Term
| Many humans carry ______ in their nasopharynx. |
|
Definition
|
|
Term
| Many humans carry Staphylococcus aureus in their ______. |
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Definition
|
|
Term
| When it swims, it projects light downward. |
|
Definition
|
|
Term
| some details about the Hawaiian Bobtailed Squid |
|
Definition
-found in the warm waters of Hawaiian coast.
-nocturnal
-When it is active at night it projects light produced by the bacteria Aliivibrio fischeri downward so its predators can't see it. That is, it projects light of the same intensity as moonlight. Doing so means it won’t cast a shadow as it swims. Its predators (such as sharks) don’t see its shadow and thus, don’t notice it. It’s a survival mechanism. |
|
|
Term
| the Hawaiian Bobtailed Squid's survival mechanism |
|
Definition
| -When it swims it projects downward light about the same light of the same intensity as moonlight so that it won’t cast a shadow as it swims, making its predators (such as sharks) unable to see it. |
|
|
Term
| the light source in the Hawaiian Bobtailed Squid |
|
Definition
| The bacteria Aliivibrio fischeri living within the squid produce the light. |
|
|
Term
| how the bacteria Aliivibrio fischeri grows inside the Hawaiian Bobtailed Squid |
|
Definition
-During the day as the squid is buried in the sand the bacteria grow to high numbers in the squid light organ. This is so at night the levels of bacteria are high enough to produce the light needed for camouflage.
-At dawn (morning) the squid will flush most of the bacteria out of the light organ (note the levels of bacteria drop). As it rests in the sand during the day the few bacteria that were not flushed out reproduce and repopulate the light organ and the cycle repeats. |
|
|
Term
| depiction of how molecular regulation in the Hawaiian Bobtailed Squid works |
|
Definition
|
|
Term
|
Definition
| the accumulation of a secreted small molecule called an autoinducer. |
|
|
Term
|
Definition
| A secreted molecule that induces quorum-sensing behavior in bacteria |
|
|
Term
| when the secreted autoinducer reenters cells |
|
Definition
| when it is at a certain extracellular concentration |
|
|
Term
| what the autoinducer does when it reenters the cell |
|
Definition
| It binds to a regulatory molecule |
|
|
Term
| the regulatory molecule the autoinducer binds to in Alliivibrio fischeri |
|
Definition
|
|
Term
|
Definition
| binds to LuxR in Alliivibrio fischeri to activate transcription of luciferase (bioluminescence) |
|
|
Term
|
Definition
| the light-producing bacteria in the Hawaiian Bobtailed Squid |
|
|
Term
| Light production by Alliivibrio fischeri requires... |
|
Definition
quorum sensing
That is, the bacteria can sense when the population is at high density and communicate with each other to produce the light (at night in this case). |
|
|
Term
| how quorum sensing works in Alliivibrio fischeri |
|
Definition
1. The LuxI protein synthesizes an acyl homoserine lactone autoinducer (AI).
2. AI diffuses into medium and accumulates.
3. At threshold concentration, AI diffuses into cell and binds LuxR, which activates lux + transcription.
[image] |
|
|
Term
| The ______ system of Alliivibrio fischeri mediates that organism’s bioluminescence. |
|
Definition
|
|
Term
|
Definition
| bind to regulatory sequences in the DNA and prevent transcription of target genes |
|
|
Term
| repressor requires ligand (______) to release |
|
Definition
|
|
Term
|
Definition
| Increased transcription of target genes caused by an inducer binding to a repressor and preventing repressor-operator binding |
|
|
Term
|
Definition
| A small molecule that must bind to a repressor to allow the repressor to bind operator DNA |
|
|
Term
|
Definition
| An increase in gene expression caused by the decrease in concentration of a corepressor |
|
|
Term
| difference between induction and derepression |
|
Definition
induction is caused by increased concentration of a ligand (inducer) while derepression is caused by decreased concentration of a ligand (corepressor)
[image] |
|
|
Term
induction or derepression?
[image] |
|
Definition
|
|
Term
induction or derepression?
[image] |
|
Definition
|
|
Term
|
Definition
bind to regulatory sequences in the DNA and stimulate transcription of target genes
Most must first bind a small ligand. |
|
|
Term
| Most activators must first... |
|
Definition
|
|
Term
| Activators bind to specific ligand and touch... |
|
Definition
| RNA polymerases sitting near promoters |
|
|
Term
| can inducers be involved in activation? |
|
Definition
yes
inducers bind to activator proteins
[image] |
|
|
Term
| sensor kinases in the cell membrane |
|
Definition
-Bind to environmental signals
-Regulate cytoplasmic events via phosphorylation |
|
|
Term
| how two-component signal transduction systems sense the external environment |
|
Definition
1. Sensor kinase detects condition outside the cell.
2. Signal triggers (or prevents) autophosphorylation.
3. Phosphate is transferred to a response regulator in the cytoplasm. Regulator binds DNA and either stimulates or represses the target genes.
4. A phosphatase removes the phosphate and down-regulates the system.
[image] |
|
|
Term
| Response regulator in the cytoplasm |
|
Definition
-Takes phosphate from sensor
-Binds chromosome, which alters transcription rate for gene(s) |
|
|
Term
| Jacques Monod and François Jacob |
|
Definition
-1961
-proposed the revolutionary idea that genes could be regulated.
-They noticed that, in E. coli, enzymes used to metabolize lactose were inducible. These enzymes were produced only when lactose was added to media.
-noted glucose enzymes were different from that of lactose
-noticed that, in E. coli, enzymes used to metabolize glucose were constitutive, which means it's produced all the time |
|
|
Term
| -proposed the revolutionary idea that genes could be regulated |
|
Definition
| Jacques Monod and François Jacob |
|
|
Term
| -noticed that, in E. coli, enzymes used to metabolize lactose were inducible. These enzymes were produced only when lactose was added to media. |
|
Definition
| Jacques Monod and François Jacob |
|
|
Term
| how lactose is moved into an E. coli cell |
|
Definition
| A lactose permease uses PMF to move lactose into cell. |
|
|
Term
|
Definition
| uses proton motive force to move lactose (and a proton) into the cell |
|
|
Term
| how a cell absorbs and processes lactose |
|
Definition
1: A dedicated lactose permease uses proton motive force to move lactose (and a proton) into the cell.
2: The enzyme beta-galactosidase (LacZ) cleaves the disaccharide into its component parts (galactose and glucose) or alters the linkage between the monosaccharides to produce allolactose, an important chemical needed to induce the genes that encode the pathway associated with the lac operon.
[image] |
|
|
Term
|
Definition
cleaves lactose into galactose and glucose at high β–galactosidase levels or...
modifies linkage producing allolactose at low β–galactosidase levels |
|
|
Term
| when β-galactosidase cleaves lactose into galactose and glucose |
|
Definition
| Only at high β–galactosidase levels |
|
|
Term
| when β-galactosidase modifies linkage in lactose to produce allolactose |
|
Definition
| Only at low β–galactosidase levels |
|
|
Term
| does the bacterium transcribe and translate the genes for lactose utilization when it doesn’t need to? |
|
Definition
| yes, but to a very small extent |
|
|
Term
| how the LacZYA OPERON is organized |
|
Definition
| lacI and lacZYA are separate transcriptional units, each with its own promoter.
[image] |
|
|
Term
| When there is no lactose, LacZYA operon is transcribed at ______ levels. |
|
Definition
very low
Thus, levels of Lactose permease and Beta-galactosidase will be very low. |
|
|
Term
| how the LacZYA OPERON is repressed in the absence of lactose |
|
Definition
The Lacl tetrameric repressor binds to specific DNA sites (the operator: lacO).
[image] |
|
|
Term
| levels of Lactose permease in the absence of lactose |
|
Definition
|
|
Term
| levels of Beta-galactosidase in the absence of lactose |
|
Definition
|
|
Term
| how the LacZYA OPERON is induced in the presence of lactose |
|
Definition
Inducer (lactose converted to allolactose) binds LacI repressor. This reduces LacI affinity for lacO, and transcription of the operon occurs.
[image] |
|
|
Term
| induction of the the LacZYA OPERON can be enhanced by... |
|
Definition
|
|
Term
| noted glucose enzymes were different from that of lactose |
|
Definition
| Jacques Monod and François Jacob |
|
|
Term
| noticed that, in E. coli, enzymes used to metabolize glucose were constitutive, which means it's produced all the time |
|
Definition
| Jacques Monod and François Jacob |
|
|
Term
|
Definition
|
|
Term
| In E.coli, ______ is the preferred carbon source. |
|
Definition
|
|
Term
| Diauxic growth results when... |
|
Definition
| both carbon sources, lactose and glucose, are present |
|
|
Term
|
Definition
| A biphasic cell growth curve caused by depletion of the favored carbon source and a metabolic switch to the second carbon source |
|
|
Term
|
Definition
| when an operon enabling the catabolism of one nutrient is repressed by the presence of a more favorable nutrient |
|
|
Term
| depiction of a diauxic growth curve |
|
Definition
|
|
Term
what does this represent?
[image] |
|
Definition
|
|
Term
| the protein yielded by LacZ |
|
Definition
|
|
Term
| the protein yielded by LacY |
|
Definition
|
|
Term
| what removes the repressor from the lac operon? |
|
Definition
|
|
Term
| What is happening at the time point circled in red? [image] |
|
Definition
-this is when the repressor gets removed, so it takes time
-this is basically where E. coli is switching gears |
|
|
Term
| Glucose ______ β-galactosidase production. |
|
Definition
|
|
Term
| Glucose transport into the cell ______ lactose import. |
|
Definition
|
|
Term
|
Definition
| The ability of glucose to cause metabolic changes that prevent the cellular uptake of less favorable carbon sources that could cause unnecessary induction. |
|
|
Term
| example of Inducer Exclusion |
|
Definition
Glucose transport into the cell inhibits lactose import.
[image] |
|
|
Term
| Glucose transport via the phosphotransferase system ______ LacY (lactose permease) |
|
Definition
|
|
Term
| how lactose import is inhibited in the presence of glucose |
|
Definition
-Phosphoenolpyruvate (PEP) “feeds” phosphate into the PTS, which relays the phosphate to glucose during transport.
-Glucose moves from protein IIC to IIB, which transfers a phosphate from IIA to glucose.
-Unphosphorylated IIAGlc inhibits LacY (lactose permease). [image] |
|
|
Term
| In the ______ of glucose the lactose transporter is fully functional to move lactose into the cell. |
|
Definition
|
|
Term
| In the absence of glucose the lactose transporter is ______ to move lactose into the cell. |
|
Definition
|
|
Term
| Absence of glucose ______ free lactose transport into the cell. |
|
Definition
|
|
Term
| ______ of glucose allows free lactose transport into the cell. |
|
Definition
|
|
Term
| how the absence of glucose allows the cell to take in lactose |
|
Definition
-In the absence of glucose, phosphorylated IIA accumulates and LacY is free to transport lactose.
-In the absence of glucose, the phosphorylated forms of glucose-specific IIAGlc and IIBCGlc accumulate and cannot inhibit LacY, which transports lactose
-LacY transports lactose, and the lac operon is induced. |
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